Table of Content:Part 1: BackgroundChapter 1 Molecular biology primer - DcrNA, RNA, Protein, Gene, Transcription, bioengineering, computing in bioengineeringChapter 2 Math background2.1 Linear algebra2.2 Probabilities - Bayes formula, stochastic process, Markov chain2.3 Optimization - Lagrange theory2.4 Statistics - machine learning, key theorem of learning theory2.5 Growth functionPart 2 Sequence analysisChapter 3 Methods for comparing sequences3.1 Similarity of sequences3.2 Dot matrix sequence comparision3.3 Overview for comparing sequences3.4 Global dynamic programming algorithm 3.5 Local dynamic programming algorithm3.6 Scoring matrices and gap penalties in sequence alignment - global, local3.7 CheckPoint algorithm3.8 FASTA, BLAST3.9 Multi-sequence alignment - MAS, the Gibbs sampler, progressive methods of multiple sequence alignment3. 10 Nucleic acid PAM scoring matrix3.11 SummaryChapter 4 Parallel computing for comparing sequences4.1 Parallel programming model4.2 Parallel computing structure4.3 Sequence comparing parallelization4.4 Smith-Waterman algorithms4.5 Data searching - FASTA, TurboBLAST, mpiBLAST4.6 Multi-sequence comparision - HMMER, ClustalW, ClusterW-MPI4.7 Sequence comparing based on specialized hardware - FPGA hardware and parallel computingChapter 5 Sequence comparison based on exact matchingChapter 6 Gene finding6.1 Algorithms for gene finding and prediction 6.2 Accuracy for prediction algorithm6.3 Methods of finding DNA sequences - open reading framesChapter 7 Markov chain and Hidden Markov model7.1 Markov chain7.2 Hidden Markov model7.3 Forward algorithms and backward algorithms7.4 Viterbi algorithm7.5 Baum-Welch algorithm, Mamitsuka algorithm7.6 HMM - using HMM to modeling Chapter 8 Models for sequence evolution8.1 Model for nucleotide replacement 8.2 Continuous time model - Jukes-Cantor, Kimura, Felsenstein, HKY8.3 Discrete time model - Jukes-Cantor, Kimura, Felsenstein, HKYChapter 9 Structuring phylogenetic tree9.1 What is phylogenetic tree? - concepts9.2 Phylogenetic inference based on distance methods9.3 Phylogenetic inference based on statistical methods9.4 Searching algorithm for tree topological spaces9.5 Phylogenetic inference using maximum likelihood methods9.6 Model selection and pretesting9.7 Phylogenetic tree structure estimation and testing
